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Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis.

Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker LV, van Leenen D, Holstege FC, Kemmeren P - BMC Genomics (2012)

Bottom Line: In general, the mutations do not induce pathway-specific transcriptional responses.Epistasis analysis of tps2Δ double mutants supports this prediction.Although based on transcriptional changes only, these results suggest that all changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, the Netherlands.

ABSTRACT

Background: Cellular glucose availability is crucial for the functioning of most biological processes. Our understanding of the glucose regulatory system has been greatly advanced by studying the model organism Saccharomyces cerevisiae, but many aspects of this system remain elusive. To understand the organisation of the glucose regulatory system, we analysed 91 deletion mutants of the different glucose signalling and metabolic pathways in Saccharomyces cerevisiae using DNA microarrays.

Results: In general, the mutations do not induce pathway-specific transcriptional responses. Instead, one main transcriptional response is discerned, which varies in direction to mimic either a high or a low glucose response. Detailed analysis uncovers established and new relationships within and between individual pathways and their members. In contrast to signalling components, metabolic components of the glucose regulatory system are transcriptionally more frequently affected. A new network approach is applied that exposes the hierarchical organisation of the glucose regulatory system.

Conclusions: The tight interconnection between the different pathways of the glucose regulatory system is reflected by the main transcriptional response observed. Tps2 and Tsl1, two enzymes involved in the biosynthesis of the storage carbohydrate trehalose, are predicted to be the most downstream transcriptional components. Epistasis analysis of tps2Δ double mutants supports this prediction. Although based on transcriptional changes only, these results suggest that all changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.

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Tps2 is epistatic to both Gpr1 and Ram1. Transcriptional changes upon the single deletion of either TPS2 or GPR1, as well as TPS2 or RAM1 are compared to the effect of their combined deletion. Shown are all transcripts (horizontal) changing significantly (p < 0.01, FC > 1.7) in any of the three deletion mutants (vertical). In both tps2Δgpr1Δ and tps2Δram1Δ double deletions, transcriptional changes of tps2Δ dominate the double mutant gene expression profile. Colour scale as in Figure 2.
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Figure 6: Tps2 is epistatic to both Gpr1 and Ram1. Transcriptional changes upon the single deletion of either TPS2 or GPR1, as well as TPS2 or RAM1 are compared to the effect of their combined deletion. Shown are all transcripts (horizontal) changing significantly (p < 0.01, FC > 1.7) in any of the three deletion mutants (vertical). In both tps2Δgpr1Δ and tps2Δram1Δ double deletions, transcriptional changes of tps2Δ dominate the double mutant gene expression profile. Colour scale as in Figure 2.

Mentions: Trehalose is synthesised by a complex consisting of four members: the trehalose-6-phosphate synthase Tps1, the trehalose-6-phosphate phosphatase Tps2, as well as the regulatory subunits Tsl1 and Tps3. Tps1 is essential for growth on rapid fermentative carbon source as used in this study, and therefore a gene expression profile of tps1Δ could not be determined. Of the remaining complex members only deletion of either Tps2 or Tsl1 leads to significant transcript changes, suggesting that Tps3 is not required for the functioning of the complex under high glucose conditions. The transcriptional regulation of Tps2 may account for the global transcriptional changes measured upon the deletion of various components of the glucose regulatory system. To further investigate this prediction, we performed epistasis analysis by gene expression profiling double mutants. These mutants consisted of tps2Δ in combination with the deletion of GPR1 and RAM1, two members of the Gpr1/PKA and Ras/PKA pathways that have a gene expression profile opposite to tps2Δ. Epistasis can describe a genetic interaction between two genes, in which the deletion of one gene masks or suppresses the effects of the other gene [42]. Tps2 is then epistatic to and in fact acting downstream of Gpr1 and Ram1 if the gene expression profile of the respective double mutant resembles the profile of the tps2Δ single mutant. Gpr1 indeed functions upstream of Tps2 as reflected in the gene expression profile of the tps2Δ gpr1Δ double mutant, which is most similar to the tps2Δ profile and the inverse of the gpr1Δ profile (Figure 6, top). Similarly, based on the transcriptional hierarchy, Ram1 would be placed upstream of Tps2, in agreement with its role in membrane anchoring of the Ras proteins. The validity of this prediction is shown by the tps2Δ ram1Δ double mutant, which is again most similar to the tps2Δ gene expression profile (Figure 6, bottom). One exception is a set of genes enriched for the GO biological process “response to pheromone” (p = 8.50E-13), which can be accounted for by Ram1 being known to also prenylate the a-factor mating pheromone (Figure 6, grey bar) [40]. The decreased transcription of these genes are the only remainder of the ram1Δ single mutant that is retained in the tps2Δ ram1Δ double mutant gene expression profile and appears to be mediated independently of Tps2. While the precise function of Tsl1 is largely unknown, the network analysis suggests that it plays an important role in communicating a feedback signal to other components of the glucose regulatory system (Figure 5E). The balance between glycogen mobilisation and trehalose biosynthesis in particular is predicted to be mediated by Tsl1 through feedback (Figure 7) as further discussed below.


Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis.

Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker LV, van Leenen D, Holstege FC, Kemmeren P - BMC Genomics (2012)

Tps2 is epistatic to both Gpr1 and Ram1. Transcriptional changes upon the single deletion of either TPS2 or GPR1, as well as TPS2 or RAM1 are compared to the effect of their combined deletion. Shown are all transcripts (horizontal) changing significantly (p < 0.01, FC > 1.7) in any of the three deletion mutants (vertical). In both tps2Δgpr1Δ and tps2Δram1Δ double deletions, transcriptional changes of tps2Δ dominate the double mutant gene expression profile. Colour scale as in Figure 2.
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Figure 6: Tps2 is epistatic to both Gpr1 and Ram1. Transcriptional changes upon the single deletion of either TPS2 or GPR1, as well as TPS2 or RAM1 are compared to the effect of their combined deletion. Shown are all transcripts (horizontal) changing significantly (p < 0.01, FC > 1.7) in any of the three deletion mutants (vertical). In both tps2Δgpr1Δ and tps2Δram1Δ double deletions, transcriptional changes of tps2Δ dominate the double mutant gene expression profile. Colour scale as in Figure 2.
Mentions: Trehalose is synthesised by a complex consisting of four members: the trehalose-6-phosphate synthase Tps1, the trehalose-6-phosphate phosphatase Tps2, as well as the regulatory subunits Tsl1 and Tps3. Tps1 is essential for growth on rapid fermentative carbon source as used in this study, and therefore a gene expression profile of tps1Δ could not be determined. Of the remaining complex members only deletion of either Tps2 or Tsl1 leads to significant transcript changes, suggesting that Tps3 is not required for the functioning of the complex under high glucose conditions. The transcriptional regulation of Tps2 may account for the global transcriptional changes measured upon the deletion of various components of the glucose regulatory system. To further investigate this prediction, we performed epistasis analysis by gene expression profiling double mutants. These mutants consisted of tps2Δ in combination with the deletion of GPR1 and RAM1, two members of the Gpr1/PKA and Ras/PKA pathways that have a gene expression profile opposite to tps2Δ. Epistasis can describe a genetic interaction between two genes, in which the deletion of one gene masks or suppresses the effects of the other gene [42]. Tps2 is then epistatic to and in fact acting downstream of Gpr1 and Ram1 if the gene expression profile of the respective double mutant resembles the profile of the tps2Δ single mutant. Gpr1 indeed functions upstream of Tps2 as reflected in the gene expression profile of the tps2Δ gpr1Δ double mutant, which is most similar to the tps2Δ profile and the inverse of the gpr1Δ profile (Figure 6, top). Similarly, based on the transcriptional hierarchy, Ram1 would be placed upstream of Tps2, in agreement with its role in membrane anchoring of the Ras proteins. The validity of this prediction is shown by the tps2Δ ram1Δ double mutant, which is again most similar to the tps2Δ gene expression profile (Figure 6, bottom). One exception is a set of genes enriched for the GO biological process “response to pheromone” (p = 8.50E-13), which can be accounted for by Ram1 being known to also prenylate the a-factor mating pheromone (Figure 6, grey bar) [40]. The decreased transcription of these genes are the only remainder of the ram1Δ single mutant that is retained in the tps2Δ ram1Δ double mutant gene expression profile and appears to be mediated independently of Tps2. While the precise function of Tsl1 is largely unknown, the network analysis suggests that it plays an important role in communicating a feedback signal to other components of the glucose regulatory system (Figure 5E). The balance between glycogen mobilisation and trehalose biosynthesis in particular is predicted to be mediated by Tsl1 through feedback (Figure 7) as further discussed below.

Bottom Line: In general, the mutations do not induce pathway-specific transcriptional responses.Epistasis analysis of tps2Δ double mutants supports this prediction.Although based on transcriptional changes only, these results suggest that all changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, the Netherlands.

ABSTRACT

Background: Cellular glucose availability is crucial for the functioning of most biological processes. Our understanding of the glucose regulatory system has been greatly advanced by studying the model organism Saccharomyces cerevisiae, but many aspects of this system remain elusive. To understand the organisation of the glucose regulatory system, we analysed 91 deletion mutants of the different glucose signalling and metabolic pathways in Saccharomyces cerevisiae using DNA microarrays.

Results: In general, the mutations do not induce pathway-specific transcriptional responses. Instead, one main transcriptional response is discerned, which varies in direction to mimic either a high or a low glucose response. Detailed analysis uncovers established and new relationships within and between individual pathways and their members. In contrast to signalling components, metabolic components of the glucose regulatory system are transcriptionally more frequently affected. A new network approach is applied that exposes the hierarchical organisation of the glucose regulatory system.

Conclusions: The tight interconnection between the different pathways of the glucose regulatory system is reflected by the main transcriptional response observed. Tps2 and Tsl1, two enzymes involved in the biosynthesis of the storage carbohydrate trehalose, are predicted to be the most downstream transcriptional components. Epistasis analysis of tps2Δ double mutants supports this prediction. Although based on transcriptional changes only, these results suggest that all changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.

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